GTA V Garage Bug: Rockstar Confirms Disappearing Car Glitch
Players recently went to GTAV's support team to report a very strange bug: when upgrading, and then completing a mission, many characters' personal cars are missing from the garage. There is no known way to recover a missing car once it has been deleted--either intentionally or otherwise.
The bug seems to delete cars after small triggers, including both completing a mission and driving another protagonist's car. Cars stored in one safehouse may not show up in another (cars stored at Franklin's Aunt's safehouse may not show up in Vinewood Hills).
Though Rockstar is working on resolving the issue, there is no fix. According to the support article, players can opt in to notifcations when the fix is released.
In the meantime, Rockstar Support suggests that players...
...please try to avoid parking a car in a garage, driving one already in a garage, or getting in a default vehicle, when playing as a character other than the one with your upgrades.
Given the hardfail releases we've seen this year (SimCity, FFXIV:ARR), if this is the only bug that Rockstar runs in to this release, it'll be one of the smoothest releases of the year.